B factors

Cort DOi iscn of OS duc avoraqoa B factors. vitn MD Lctuai ons... 

The relative molecular dynamics fluctuations shown in Figure 7-17 can be compared with the crystallographic B-factors, which are also called temperature factors. The latter name, especially, indicates the information content of these factors they show how well defined within the X-ray structure the position of an atom is. Atoms with high temperature have an increased mobility. In principle, this is the same information as is provided by the molecular dynamics fluctuations. Using Eq. (48), the RMS fluctuation of an atom j can be converted into a B-factor... 

A b = factor of braking, which depends upon the type of braking used, such as... 

Bahar et al. [46] have used this kind of approach to predict the B-factors of 12 X-ray structures. Elements in the Hessian corresponding to atom pairs separated by a distance of less than 7 A are set to zero, and the remainder have the same value dependent on a single adjustable parameter. Generally B-factor predictions for the a-carbons compare very well with the B-factors measured by X-ray crystallography. Figure 1 shows the result for the subunit A of endodeoxyribonuclease I complexed with actin. 

Figure 1 Experimental B-factors of a-carbon atoms (thin curve) compared with those predicted using their single-parameter model for subunit A of endodeoxyribonuclease I complexed with actm (thick curve). Calculations were performed using both subunits A and D comprising 633 residues. Their parameter is adjusted such that the area under the predicted curve equals the area under the experimental curve. (From Ref. 46.)...

B. Factors Governing Selectivity in Formation of Protecting Groups 1. Protection of carbonyl groups... 

The crystal structures of four chlorinated derivatives of di-benzo-p-dioxin have been determined by x-ray diffraction from diffractometer data (MoKa radiation). The compounds, their formulae, cell dimensions, space groups, the number of molecules per unit cell, the crystallographic B.-factors, and the number of observed reflections are given. The dioxin crystal structures were performed to provide absolute standards for assignment of isomeric structures and have been of considerable practical use in combination with x-ray powder diffraction analysis. 

Exclusion implies that criteria must be fulfilled without compromise since the study may be jeopardized if the criteria are not met Priority A implies some flexibility after careful consideration Priority B factors offer the greatest flexibility in terms of site selection. 

Cloughley, J. B., Factors influencing the caffeine content of black tea Part 1 — The effect of field variables. Food Chem., 9 69, 1982. 

The atomic temperature factor, or B factor, measures the dynamic disorder caused by the temperature-dependent vibration of the atom, as well as the static disorder resulting from subtle structural differences in different unit cells throughout the crystal. For a B factor of 15 A2, displacement of an atom from its equilibrium position is approximately 0.44 A, and it is as much as 0.87 A for a B factor of 60 A2. It is very important to inspect the B factors during any structural analysis a B factor of less than 30 A2 for a particular atom usually indicates confidence in its atomic position, but a B factor of higher than 60 A2 likely indicates that the atom is disordered. 

Figure 13-4. The crystal structure of 1ZB6 colored by B-factor values. The color scale (from blue to white to red) used has a range from 23.0 to 67.0 A2. 1,6-DHN is shown with thick cylinders with an average...

Reetz, M.T., Carballeira, J.D. and Vogel, A. (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angewandte Chemie (International Edition in English), 45, 7745-7751. 

Table 1 A and B factors for some common luminescent lanthanides (for Equations (4) and (7)).

Note that/y is time-dependent through the b factors. In the absence of reactions, b2 varies linearly with time as b2 = 2r2 + 4Dt. Because of bimolecular reactions, it must increase somewhat faster to account for the reduction of central density. Schwarz takes this effect into account by writing db2/dt = 4D. + /).( ) and devises an approximate procedure to evaluate /) by separating the contributions due to different reactions—namely,... 

The EC (pS cm-1) and the TDS (mg L ) both reflect the water ionic content, i.e. the dissolved load also called water salinity. The EC, easily obtained compared to chemical data, is thus widely documented in the CHEBRO database (n = 2,860 versus 999 complete major element analyses). These two parameters (EC and TDS) are linked by a linear relation TDS (mg L ) = b EC (pS cm-1), with a mean b factor 0.54 < b < 0.96 according to water types and range of salinity [21, 22], The linear relations between TDS and EC were calculated for each monitoring station, b factor ranging from 0.713 (Arga) and 0.86 (Aragon), whereas the Ebro River stations present less variability (0.774—0.798) with R2 always better than 0.72, all the relations are summarised in Table 1. These relations are very similar to that defined for the whole Ebro basin with b = 0.81 [23]. 

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